From: Dawid das (addiw7_at_googlemail.com)
Date: Tue Jan 27 2015 - 11:26:50 CST
Dear NAMD experts,
I want to simulate permeation of protein through silicon nitride nanopore.
I have equilibrated the system, everything was fine till I turned the field
on.
After ca. 60 steps of simulation I get an error:
ERROR: Atom 51623 velocity is 70243.6 -303988 291675 (limit is 12000, atom
390 of 1094 on patch 28 pe 0)
ERROR: Atom 86282 velocity is -998068 4.2818e+06 -4.08232e+06 (limit is
12000, atom 674 of 1094 on patch 28 pe 0)
ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on
patch 28 pe 0).
ERROR: Exiting prematurely; see error messages above.
I have done succesfully similar simulation for DNA permeation. Could you
give me a tip
where I should look for an error?
This is my input file:
# NAMD config file
numsteps 7500000
structure pore+protein_all.psf
coordinates pore+protein_all.pdb
outputName run0
XSTfile run0.xst
bincoordinates eq3.coor
binvelocities eq3.vel
extendedSystem eq3.xsc
langevin on
langevinDamping 20
langevinTemp 295
langevinHydrogen off
switching on
switchDist 10
cutoff 12
pairlistdist 14
margin 3
binaryOutput yes
binaryRestart yes
parameters par_all27_prot_na.prm
parameters par_silicon_ions_NEW5.inp
paraTypeCharmm on
wrapAll yes
wrapNearest yes
COMmotion no
outputEnergies 1
outputTiming 1
xstFreq 1
dcdFreq 1
restartFreq 1
timestep 1
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20
Pme on
PmeGridSizeX 96
PmeGridSizeY 96
PmeGridSizeZ 288
exclude scaled1-4
1-4scaling 1
constraints on
consKCol B
consref siliconRest_50.0.pdb
consKFile siliconRest_50.0.pdb
## electric field
eFieldOn on
eField 0.0 0.0 150.0
The constraint constant I use is 50 kcal/mol.
Best wishes,
Dawid Grabarek
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